Merge pull request #32 from jeromekelleher/initial-structure

Initial structure

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "c/kastore"]
+	path = c/kastore
+	url = https://github.com/tskit-dev/kastore.git

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 tskit-dev
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,15 +1,9 @@
 # tskit
 The tree sequence toolkit
 
-**This repository is a placeholder, and currently only exists to ensure the 
-  name isn't taken on PyPI.**
+**This repository is currently under heavy development.**
 
-Currently, the `tskit` tools are still bundled with the Python package [`msprime`](https://github.com/tskit-dev/msprime).
-We expect to separate the two soon,
-but to use `tskit` in the meantime, [install `msprime`](https://msprime.readthedocs.io/en/latest/installation.html),
-and then
-```
-import msprime as tskit
-```
-will get you the functionality that `tskit` will provide in the future.
+Currently, the `tskit` tools are bundled with the Python package 
+[`msprime`](https://github.com/tskit-dev/msprime) and we are in the process
+of extracting them here.
 

c/CHANGELOG.rst

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+--------------------
+[0.0.0] - 2019-01-19
+--------------------
+
+Initial extraction of tskit code from msprime. Relicense to MIT.
+Code copied at hash 29921408661d5fe0b1a82b1ca302a8b87510fd23

c/Makefile

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+CC=gcc
+CFLAGS=-g -O2 -std=c99 -pedantic -Werror -Wall -W \
+  -Wmissing-prototypes -Wstrict-prototypes \
+  -Wconversion -Wshadow -Wpointer-arith \
+  -Wcast-align -Wcast-qual \
+  -Wwrite-strings -Wnested-externs \
+  -fshort-enums -fno-common -Dinline= \
+  -Ikastore/c
+LDFLAGS=-lm
+OBJECTS=tsk_core.o tsk_tables.o tsk_trees.o tsk_genotypes.o \
+	tsk_convert.o tsk_stats.o kastore.o 
+HEADERS=tsk_core.h tsk_tables.h tsk_trees.h tsk_genotypes.h \
+	tsk_convert.h tsk_stats.h
+EXECUTABLES=main test_core test_tables test_trees test_genotypes
+
+all: old_tests ${EXECUTABLES} libtskit.a
+
+main: main.c ${OBJECTS} argtable3.o 
+	${CC} ${CFLAGS} -o $@ $^ ${LDFLAGS} 
+
+libtskit.a: ${OBJECTS}
+	ar rcs $@ $^
+
+test_%: test_%.c testlib.o ${OBJECTS}
+	${CC} ${CFLAGS} -o $@ $^ ${LDFLAGS} -lcunit
+
+tsk_%.o: tsk_%.c tsk_%.h tsk_core.h
+	${CC} ${CFLAGS} $< -c 
+
+# We can't turn on all the usual compiler checks because of CUnit.
+testlib.o: testlib.c
+	${CC} -Ikastore/c -std=c99 -Wall -g -c $^ 
+
+argtable3.o: argtable3.c
+	${CC} -Dlint -Wall -g -O2 -c argtable3.c
+
+old_tests: old_tests.c ${OBJECTS}
+	${CC} -Ikastore/c -std=c99 -Wall -g $^ ${LDFLAGS} -lcunit -lgsl -lgslcblas
+
+kastore.o: kastore/c/kastore.c
+	$(CC) -c $(CFLAGS) $(CPPFLAGS) $< 
+
+clean:
+	rm -f *.o ${EXECUTABLES}
+
+tags:
+	ctags *.c *.h